Maximum likelihood

Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes

X. - Z. Kan, Yang, J. - K., Li, X. - F., Chen, L., Lei, Z. - P., Wang, M., Qian, C. - J., Gao, H., and Yang, Z. - Y., Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes, vol. 9, pp. 1625-1633, 2010.

Complete mitochondrial DNA sequences have been used successfully to estimate phylogenetic relationships among animal taxa, and for studies of population genetics and molecular evolution. We made phylogenetic analyses of 22 species of Galliformes, with two species of Anseriformes as outgroups, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) methods based on the nucleotide dataset and the corresponding amino acid dataset of 13 concatenated protein-coding genes.

Analysis of differential selective forces acting on the coat protein (P3) of the plant virus family Luteoviridae

M. W. Torres, Corrêa, R. L., and Schrago, C. G., Analysis of differential selective forces acting on the coat protein (P3) of the plant virus family Luteoviridae, vol. 4, pp. 790-802, 2005.

The coat protein (CP) of the family Luteoviridae is directly associated with the success of infection. It participates in various steps of the virus life cycle, such as virion assembly, stability, systemic infection, and transmission. Despite its importance, extensive studies on the molecular evolution of this protein are lacking. In the present study, we investigate the action of differential selective forces on the CP coding region using maximum likelihood methods.

Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers

C. M. Voloch, Freire, P. R., and Russo, C. A. M., Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers, vol. 4, pp. 668-674, 2005.

Penaeid shrimps are an important resource in crustacean fisheries, representing more than the half of the gross production of shrimp worldwide. In the present study, we used a sample of wide-ranging diversity (41 shrimp species) and two mitochondrial markers (758 bp) to clarify the evolutionary relationships among Penaeidae genera. Three different methodologies of tree reconstruction were employed in the study: maximum likelihood, neighbor joining and Bayesian analysis.

Evolutionary tree reconstruction using structural expectation maximization and homotopy

J. Li and Guo, M., Evolutionary tree reconstruction using structural expectation maximization and homotopy, vol. 6, pp. 522-533, 2007.

The evolutionary tree reconstruction algorithm called SEMPHY using structural expectation maximization (SEM) is an efficient approach but has local optimality problem. To improve SEMPHY, a new algorithm named HSEMPHY based on the homotopy continuation principle is proposed in the present study for reconstructing evolutionary trees. The HSEMPHY algorithm computes the condition probability of hidden variables in the structural through maximum entropy principle.

Subscribe to Maximum likelihood